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Donnelly was the son of Philip Carrol Donnelly, an Irish Catholic immigrant who had settled in Philadelphia, Pennsylvania. His sister was the writer Eleanor C. Donnelly. On June 29, 1826, Philip had married Catherine Gavin, a second generation American of Irish ancestry.

After starting as a peddler, Philip studied medicine at the Philadelphia College of Medicine. He later contracted typhus from a patient and died at age 31, leaving his wife with five children.

Catherine provided for her children by operating a pawn shop. Ignatius, her youngest son, was admitted to the prestigious Central High School, the second oldest public high school in the United States. There he studied under the presidency of John S. Hart, excelling primarily in literature.

Donnelly decided to become a lawyer, and became a clerk for Benjamin Brewster, who later became Attorney-General of the United States. Donnelly was admitted to the bar in 1852. In 1855, he married Katherine McCaffrey, with whom he had three children. In 1855, he resigned his clerkship, entered politics, and participated in communal home building schemes. He quit the Catholic Church some time in the 1850s, and thereafter was never active in any religious group.[1]

Donnelly entered politics and was lieutenant governor of Minnesota from 1860–1863. He was a Radical Republican Congressman from Minnesota in the 38th, 39th, and 40th congresses, (1863–1869), a state senator from 1874–1878 and 1891-1894 and a state representative from 1887-1888 and 1897-1898.[3] As a legislator, he advocated extending the powers of the Freedmen's Bureau to provide education for freedmen so that they could protect themselves once the bureau was withdrawn. Donnelly was also an early supporter of women's suffrage. After leaving the Minnesota State Senate in 1878, he returned to his law practice and writing.

A year after Atlantis, he published Ragnarok: The Age of Fire and Gravel, in which he expounded his belief that the Flood (as well as the destruction of Atlantis and the extinction of the mammoth) had been brought about by the near-collision of the earth with a massive comet. This book also sold well, and both books seem to have had an important influence on the development of Immanuel Velikovsky's controversial ideas half a century later.

In 1888, he published The Great Cryptogram in which he proposed that Shakespeare's plays had been written by Francis Bacon, an idea that was popular during the late 19th and early 20th century. He then travelled to England to arrange the English publication of his book by Sampson Low, speaking at the Oxford (and Cambridge) Union, where his thesis "Resolved, that the works of William Shakespeare were composed by Francis Bacon" was put to an unsuccessful vote. The book was a complete failure and Donnelly was discredited.

Donnelly also made several other campaigns for public office during the 1880s. He made a losing campaign for Congress (this time as a Democrat) in 1884. In 1887, he successfully campaigned for a seat in the Minnesota State Legislature as an Independent. During this period, he was also an organizer of the Minnesota Farmers' Alliance.

The People's Party protested the railroad companies corrupting government, and advocated government regulation of the railroads. Donnelly had a key leadership role in this party, yet he received $10,000 from the Lake Superior and Mississippi Railroad Company.[4]

During the 1930s, an organization was formed to lobby for the creation of a state park at Donnelly's home at Nininger near Hastings, Minnesota. The house was still standing in 1939, but the effort failed and the house has since been demolished.[5]